I have long been disappointed in the ability of most RPGs to handle rules for supers. Most **system’s rules heavy approach just don’t deal with the wide range of abilities that can pop up very well. However, with very minimal adaptation Spirits of the Century the can be used to run a supers game due to its cinematic nature quite well.
I treat each super power as a new skill and use custom stunts to further define the power. This works best in a pulp setting as it allows for a highly skilled hero (Batman) to take on a true power house (Hulk) since their skill trees are on the same scale. To create a tiered scale between heroes you can cap the level of the powers skill. Top flight heroes can have Superb powers while weaker heroes would not be able to have their powers higher the Good. You can also create a difference between supers and normals by capping the level of skills for normals.
For example, I made a Blaster who shoots energy beams of some sort. His power is Energy Blast rated at Superb. His power stunts I ripped right from the Guns stunts: Long Shot and Trick Shot.
For an example where I really hacked the rules, I made a guy who makes clones of himself like Multiple Man. His skill is Cloning, and without stunts he can make copies of himself splitting off one box from his health and composure track for each clone. If they get hit they are taken out, no consequences. Then I gave him the stunt Superior Clones which lets him divide up his Health/Composure tracks anyway he wants. He can make 5 other clones all with one box each and actually get a bonus for attacking as a group but he is easy to take out that way. There was not a whole lot of room for the players to customize this power, but they decided that since he has one more box of health then composure that he can make a #6 clone that is, well lets say dim witted.

Sample Powers and Stunts:

Elemental Aura: Able to generate and manipulate Ice, Fire, or Lightning

Cold Snap: Create intense cold in the characters current zone damaging everyone in it, friend and foe. Everyone other then the character must make an endurance contest versus the Elemental Aura of the character.

Id Projection: The player can create a semi solid manifestation of his ID, pure aggression and base instinct. The projection can perform any physical skill at the Id Projection level. Any stress or consequences suffered by the projection are suffered by the character.

Brawler: Just as the Fists stunt but for the Id Projected figure.

Shape Shifting: The character can shape shift into any animal, but not other humans.

Bestial Skill: The character can use Shape Shifting in place of another skill in his pyramid if he can find an animal form that can perform the skill.

Adaptation: The character can use Shape Shifting in place of another skill that is not in his pyramid by spending a Fate Point.

Power Negation: The character can prevent others from using their super powers. Target number is the skill level of the power to be negated. Any extra shifts can be used to extend the duration of the negation by one round per shift.

Teleportation: The character can move by teleportation.

Long Range Teleport: The character gets +2 on his Teleportation roll if used for a sprint action.

Teleport Strike: The character can use teleport as a complimentary action to make an attack without the -1 to the skill check.